Yong-Joon Cho

Seoul National University, Sŏul, Seoul, South Korea

Are you Yong-Joon Cho?

Claim your profile

Publications (35)97.66 Total impact

  • Brett Bowman · Mincheol Kim · Yong-Joon Cho · Jonas Korlach
    [Show abstract] [Hide abstract]
    ABSTRACT: In this chapter, we describe applications of single molecule, real-time (SMRT) DNA sequencing toward metagenomic research. The long sequence reads, combined with a lack of bias with respect to DNA sequence context or GC content, facilitate a more comprehensive analysis of the genomic constitution of microbial communities. Full-length 16S RNA gene sequencing at high (>99%) accuracy allows for species-level characterization of community members concomitant with the determination of community structure. The application of SMRT sequencing to whole-community shotgun microbial metagenomics has also been discussed.
    No preview · Chapter · Dec 2015
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Mycobacterium tuberculosis K, a member of the Beijing family, was first identified in 1999 as the most prevalent genotype in South Korea among clinical isolates of M. tuberculosis from high school outbreaks. M. tuberculosis K is an aerobic, non-motile, Gram-positive, and non-spore-forming rod-shaped bacillus. A transmission electron microscopy analysis displayed an abundance of lipid bodies in the cytosol. The genome of the M. tuberculosis K strain was sequenced using two independent sequencing methods (Sanger and Illumina). Here, we present the genomic features of the 4,385,518-bp-long complete genome sequence of M. tuberculosis K (one chromosome, no plasmid, and 65.59 % G + C content) and its annotation, which consists of 4194 genes (3447 genes with predicted functions), 48 RNA genes (3 rRNA and 45 tRNA) and 261 genes with peptide signals. Electronic supplementary material The online version of this article (doi:10.1186/s40793-015-0071-4) contains supplementary material, which is available to authorized users.
    Full-text · Article · Oct 2015 · Standards in Genomic Sciences
  • Su-Kyoung Shin · Chung Yeon Hwang · Yong-Joon Cho · Hana Yi
    [Show abstract] [Hide abstract]
    ABSTRACT: Serpens flexibilis was proposed in 1977 and approved in 1980 without the 16S rRNA gene sequence information. The sequence of S. flexibilis became available in 2010, after the publication of Pseudomonas tuomuerensis in 2009. Our preliminary phylogenetic analyses indicated that these two strains share high sequence similarity and therefore showed strong potential to be united into a single species. To clarify the taxonomic status of the two species, a polyphasic taxonomy study was conducted including whole genome sequencing. The value of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between the genome sequences of S. flexibilis ATCC 29606(T) and P. tuomuerensis JCM 14085(T) were 98.1% and 89.0%, respectively. The phenotypic and chemotaxonomic properties including enzymatic activities, substrate utilization profiles, and fatty acids, supported that the two taxa have no pronounced difference and should thus constitute a single species. Therefore, we propose to transfer Serpens flexibilis Hespell 1977 to the genus Pseudomonas as Pseudomonas flexibilis comb. nov. (type strain=ATCC 29606(T)), with Pseudomonas tuomuerensis Xin et al. 2009 as a later heterotypic synonym of Pseudomonas flexibilis.
    No preview · Article · Oct 2015 · Systematic and Applied Microbiology
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Haloterrigena jeotgali is a halophilic archaeon within the family Natrialbaceae that was isolated from shrimp jeotgal, a traditional Korean salt-fermented food. A29(T) is the type strain of H. jeotgali, and is a Gram-negative staining, non-motile, rod-shaped archaeon that grows in 10 %-30 % (w/v) NaCl. We present the annotated H. jeotgali A29(T) genome sequence along with a summary of its features. The 4,131,621 bp genome with a GC content of 64.9 % comprises 4,215 protein-coding genes and 127 RNA genes. The sequence can provide useful information on genetic mechanisms that enable haloarchaea to endure a hypersaline environment.
    Preview · Article · Sep 2015 · Standards in Genomic Sciences
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: An extremely halophilic archaeon, Haladaptatus cibarius D43(T), was isolated from traditional Korean salt-rich fermented seafood. Strain D43(T) shows the highest 16S rRNA gene sequence similarity (98.7 %) with Haladaptatus litoreus RO1-28(T), is Gram-negative staining, motile, and extremely halophilic. Despite potential industrial applications of extremely halophilic archaea, their genome characteristics remain obscure. Here, we describe the whole genome sequence and annotated features of strain D43(T). The 3,926,724 bp genome includes 4,092 protein-coding and 57 RNA genes (including 6 rRNA and 49 tRNA genes) with an average G + C content of 57.76 %.
    Full-text · Article · Sep 2015 · Standards in Genomic Sciences
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The full genome sequence of a Middle East respiratory syndrome coronavirus (MERS-CoV) was identified from cultured and isolated in Vero cells. The viral genome sequence has high similarity to 53 human MERS-CoVs, ranging from 99.5% to 99.8% at the nucleotide level.
    Full-text · Article · Aug 2015 · Genome Announcements
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Flavobacterium seoulense strain EM1321(T) is the type strain of Flavobacterium seoulense sp. nov., a proposed novel species within the genus Flavobacterium. This strain is a Gram-reaction-negative, aerobic, rod-shaped bacterium isolated from stream water in Bukhansan National Park, Seoul. This organism is motile by gliding. Here, we describe the features of Flavobacterium seoulense EM1321(T), together with its genome sequence and annotation. The genome comprised 3,792,640 bp, with 3,230 protein-coding genes and 52 RNA genes.
    Preview · Article · Dec 2014 · Standards in Genomic Sciences
  • Source
    Hana Yi · Dongeun Yong · Kyungwon Lee · Yong-Joon Cho · Jongsik Chun
    [Show abstract] [Hide abstract]
    ABSTRACT: Background Infection by pathogenic viruses results in rapid epithelial damage and significantly impacts on the condition of the upper respiratory tract, thus the effects of viral infection may induce changes in microbiota. Thus, we aimed to define the healthy microbiota and the viral pathogen-affected microbiota in the upper respiratory tract. In addition, any association between the type of viral agent and the resultant microbiota profile was assessed.Methods We analyzed the upper respiratory tract bacterial content of 57 healthy asymptomatic people (17 health-care workers and 40 community people) and 59 patients acutely infected with influenza, parainfluenza, rhino, respiratory syncytial, corona, adeno, or metapneumo viruses using culture-independent pyrosequencing.ResultsThe healthy subjects harbored primarily Streptococcus, whereas the patients showed an enrichment of Haemophilus or Moraxella. Quantifying the similarities between bacterial populations by using Fast UniFrac analysis indicated that bacterial profiles were apparently divisible into 6 oropharyngeal types in the tested subjects. The oropharyngeal types were not associated with the type of viruses, but were rather linked to the age of the subjects. Moraxella nonliquefaciens exhibited unprecedentedly high abundance in young subjects aged <6 years. The genome of M. nonliquefaciens was found to encode various proteins that may play roles in pathogenesis.Conclusions This study identified 6 oropharyngeal microbiome types. No virus-specific bacterial profile was discovered, but comparative analysis of healthy adults and patients identified a bacterium specific to young patients, M. nonliquefaciens.
    Preview · Article · Nov 2014 · BMC Infectious Diseases
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Leucobacter salsicius M1-8(T) is a member of the Microbacteriaceae family within the class Actinomycetales. This strain is a Gram-positive, rod-shaped bacterium and was previously isolated from a Korean fermented food. Most members of the genus Leucobacter are chromate-resistant and this feature could be exploited in biotechnological applications. However, the genus Leucobacter is poorly characterized at the genome level, despite its potential importance. Thus, the present study determined the features of Leucobacter salsicius M1-8(T), as well as its genome sequence and annotation. The genome comprised 3,185,418 bp with a G+C content of 64.5%, which included 2,865 protein-coding genes and 68 RNA genes. This strain possessed two predicted genes associated with chromate resistance, which might facilitate its growth in heavy metal-rich environments.
    Preview · Article · Jun 2014 · Standards in Genomic Sciences
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Kitasatospora cheerisanensis KCTC 2395, which produces antifungal metabolites with bafilomycin derivatives, including bafilomycin C1-amide, was isolated from a soil sample at Mt. Jiri, South Korea. Here, we report its draft genome sequence, which contains 8.04 Mb with 73.6% G+C content and 7,810 protein-coding genes.
    Full-text · Article · May 2014 · Genome Announcements
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Vanillin is a well-known food and cosmetic additive and has antioxidant and antimutagenic properties. It has also been suggested to have antifungal activity against major human pathogenic fungi, although it is not very effective. In this study, the antifungal activities of vanillin and 33 vanillin derivatives against the human fungal pathogen Cryptococcus neoformans, the main pathogen of cryptococcal meningitis in immunocompromised patients, were investigated. We found a structural correlation between the vanillin derivatives and antifungal activity, showing that the hydroxyl or alkoxy group is more advantageous than the halogenated or nitrated group in benzaldehyde. Among the vanillin derivatives with a hydroxyl or alkoxy group, o-vanillin and o-ethyl vanillin showed the highest antifungal activity against C. neoformans. o-Vanillin was further studied to understand the mechanism of antifungal action. We compared the transcriptome of C. neoformans cells untreated or treated with o-vanillin by using RNA sequencing and found that the compound caused mitochondrial dysfunction and triggered oxidative stress. These antifungal mechanisms of o-vanillin were experimentally confirmed by the significantly reduced growth of the mutants lacking the genes involved in mitochondrial functions and oxidative stress response.
    Full-text · Article · Feb 2014 · PLoS ONE
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: EzEditor is a Java-based molecular sequence editor allowing manipulation of both DNA and protein sequence alignments for phylogenetic analysis. It has multiple features optimized to connect initial computer-assisted multiple alignment and subsequent phylogenetic analysis by providing manual editing with reference to biological information specific to the genes under consideration. It provides various functionality for editing rRNA alignment using secondary structure information. In addition, it supports simultaneous editing for both DNA and their translated protein sequences for protein-coding genes. EzEditor is the first sequence editing software designed for both RNA and protein coding genes with the visualization of biologically relevant information, and should be useful in molecular phylogenetic studies. EzEditor is based on Java which can be run on all major operating systems, and freely available from http://sw.ezbiocloud.net/ezeditor/.
    Preview · Article · Dec 2013 · International Journal of Systematic and Evolutionary Microbiology
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Members of the Mycobacterium abscessus complex are rapidly growing mycobacteria that are emerging as human pathogens. The M. abscessus complex was previously composed of three species, namely M. abscessus sensu stricto, ‘M. massiliense’, and ‘M. bolletii’. In 2011, ‘M. massiliense’ and ‘M. bolletii’ were united and reclassified as a single subspecies within M. abscessus: M. abscessus subsp. bolletii. However, the placement of ‘M. massiliense’ within the boundary of M. abscessus subsp. bolletii remains highly controversial with regard to clinical aspects. In this study, we revisited the taxonomic status of members of the M. abscessus complex based on comparative analysis of the whole-genome sequences of 53 strains. The genome sequence of the previous type strain of ‘Mycobacterium massiliense’ (CIP 108297) was determined using next-generation sequencing. The genome tree based on average nucleotide identity (ANI) values supported the differentiation of ‘M. bolletii’ and ‘M. massiliense’ at the subspecies level. The genome tree also clearly illustrated that ‘M. bolletii’ and ‘M. massiliense’ form a distinct phylogenetic clade within the radiation of the M. abscessus complex. The genomic distances observed in this study suggest that the current M. abscessus subsp. bolletii taxon should be divided into two subspecies, M. abscessus subsp. massiliense subsp. nov. and M. abscessus subsp. bolletii, to correspondingly accommodate the previously known ‘M. massiliense’ and ‘M. bolletii’ strains.
    Preview · Article · Nov 2013 · PLoS ONE
  • [Show abstract] [Hide abstract]
    ABSTRACT: Diketopiperazine (DKP) is produced by various organisms, including bacteria, fungi, and animals, and has been suggested as a novel signal molecule involved in the modulation of genes with various biological functions. Vibrio vulnificus, which causes septicemia in humans, produces cyclo(L-phenylalanine-L-proline) (cFP). To understand the biological roles of cFP, the effect of the compound on the expression of the total mRNA in V. vulnificus was assessed by next-generation sequencing (NGS). Based on the transcriptomic analysis, we classified the cFP-regulated genes into functional categories and clustered them according to the expression patterns resulting from treatment with cFP. From a total of 4,673 genes, excepting the genes encoding tRNA in V. vulnificus, 356 genes were up-regulated and 602 genes were down-regulated with an RPKM (reads per kilo-base per million) value above 3. The genes most highly induced by cFP comprised those associated with the transport and metabolism of inorganic molecules, particularly iron. The genes negatively regulated by cFP included those associated with energy production and conversion, as well as carbohydrate metabolism. Noticeably, numerous genes related with biofilm formation were modulated by cFP. We demonstrated that cFP interferes significantly with the biofilm formation of V. vulnificus.
    No preview · Article · Oct 2013 · Journal of Microbiology and Biotechnology
  • Source
    Yong-Joon Cho · Hana Yi · Boram Seo · Kyeung Hee Cho · Jongsik Chun
    [Show abstract] [Hide abstract]
    ABSTRACT: A brick-red colored, curved-rod shaped, prostheca-bearing and non-motile bacterial strain, designated JC2236T, was isolated from a seawater sample of Jeju Island, Korea. Result of 16S rRNA gene sequence analysis indicated that the test strain belongs to the family Hyphomonadaceae and represents a distinct phyletic line that reflects a novel genus status within a clade containing genera Litorimonas, Hellea, Robiginitomaculum and Algimonas. The predominant isoprenoid quinone (Q10) and polar lipid profile (PG, GUDG and MGDG) were in line with those of most members of the family. However, the DNA G+C content (49.3 mol%), the abundance of C16:0, the requirement of sea salts for growth, and absence of cell motility differentiated strain JC2236T from other closely related genera. Overall enzymatic traits also demonstrated that the test strain does not closely affiliate with any of the previously described genera. Thus, based on polyphasic taxonomic data, it is proposed that strain JC2236T constitute a novel genus and a novel species belonging to the family Hyphomonadaceae. The name Fretibacter rubidus gen. nov., sp. nov. is therefore proposed for the isolate; type strain is JC2236T (= KACC 16935T = JCM 15585T).
    Preview · Article · Aug 2013 · International Journal of Systematic and Evolutionary Microbiology
  • Sunhwa Park · Ji-Hoon Lee · Yong-Joon Cho · Jongsik Chun · Hor-Gil Hur
    [Show abstract] [Hide abstract]
    ABSTRACT: In previous study, alkaliphilic and thermotolerant bacterium strain, Pseudomonas sp. strain G5, capable of reducing insoluble indigo was isolated from Korean traditional fermentation liquor. Here, we report the draft genome sequence and annotation of strain G5 to provide the genomic information involved in indigo reduction process.
    No preview · Article · Jun 2013 · Journal of the Korean Society for Applied Biological Chemistry
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Salinicoccus carnicancri Jung et al. 2010 belongs to the genus Salinicoccus in the family Staphylococcaceae. Members of the Salinicoccus are moderately halophilic and originate from various salty environments. The halophilic features of the Salinicoccus suggest their possible uses in biotechnological applications, such as biodegradation and fermented food production. However, the genus Salinicoccus is poorly characterized at the genome level, despite its potential importance. This study presents the draft genome sequence of S. carnicancri strain Crm(T) and its annotation. The 2,673,309 base pair genome contained 2,700 protein-coding genes and 78 RNA genes with an average G+C content of 47.93 mol%. It was notable that the strain carried 72 predicted genes associated with osmoregulation, which suggests the presence of beneficial functions that facilitate growth in high-salt environments.
    Full-text · Article · Jun 2013 · Standards in Genomic Sciences
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Escherichia coli AI27 is a putatively commensal strain isolated from feces of a pig. Here we report the draft genome sequence of E. coli AI27. This is the first porcine strain in the phylogenetic group B1 whose genome sequence has been determined.
    Full-text · Article · Dec 2012 · Journal of bacteriology
  • [Show abstract] [Hide abstract]
    ABSTRACT: The high-affinity reductive iron uptake system that includes a ferroxidase (Cfo1) and an iron permease (Cft1) is critical for the pathogenesis of Cryptococcus neoformans. In addition, a mutant lacking CFO1 or CFT1 not only has reduced iron uptake but also displays a markedly increased susceptibility to azole antifungal drugs. Altered antifungal susceptibility of the mutants was of particular interest because the iron uptake system has been proposed as an alternative target for antifungal treatment. In this study, we used transcriptome analysis to begin exploring the molecular mechanisms of altered antifungal susceptibility in a cfo1 mutant. The wild-type strain and the cfo1 mutant were cultured with or without the azole antifungal drug fluconazole and their transcriptomes were compared following sequencing with Illumina Genome Analyzer IIx (GAIIx) technology. As expected, treatment of both strains with fluconazole caused elevated expression of genes in the ergosterol biosynthetic pathway that includes the target enzyme Erg11. Additionally, genes differentially expressed in the cfo1 mutant were involved in iron uptake and homeostasis, mitochondrial functions and respiration. The cfo1 mutant also displayed phenotypes consistent with these changes including a reduced ratio of NAD(+)/NADH and down-regulation of Fe-S cluster synthesis. Moreover, combination treatment of the wild-type strain with fluconazole and the respiration inhibitor diphenyleneiodonium dramatically increased susceptibility to fluconazole. This result supports the hypothesis that down-regulation of genes required for respiration contributed to the altered fluconazole susceptibility of the cfo1 mutant. Overall, our data suggest that iron uptake and homeostasis play a key role in antifungal susceptibility and could be used as novel targets for combination treatment of cryptococcosis. Indeed, we found that iron chelation in combination with fluconazole treatment synergistically inhibited the growth of C. neoformans.
    No preview · Article · Sep 2012 · Fungal Genetics and Biology
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: An enteric bacterium, Escherichia coli W26 (KACC 16630), was isolated from feces from a healthy cow in South Korea. Here, we report the draft genome sequence of the isolate, which is closely affiliated with commensal strains belonging to E. coli phylogroup B1.
    Full-text · Article · Sep 2012 · Journal of bacteriology

Publication Stats

2k Citations
97.66 Total Impact Points

Institutions

  • 2004-2015
    • Seoul National University
      • Department of Biological Sciences
      Sŏul, Seoul, South Korea
  • 2014
    • Kyung Hee University
      • Department of Life and Nanopharmaceutical Science
      Sŏul, Seoul, South Korea
  • 2012
    • Sungkyunkwan University
      • School of Medicine
      Sŏul, Seoul, South Korea
  • 2011-2012
    • Gwangju Institute of Science and Technology
      • School of Environmental Science and Engineering
      Gwangju, Gwangju, South Korea
    • Sahmyook University
      Sŏul, Seoul, South Korea
    • Chung-Ang University
      Sŏul, Seoul, South Korea
    • chunlab
      Sŏul, Seoul, South Korea
  • 2010
    • Inha University
      • Division of Biology and Ocean Sciences
      Sŏul, Seoul, South Korea